Using EuGeneCiD and EuGeneCiM computational tools for synthetic biology

Wheaton L Schroeder; Anna S Baber; Rajib Saha

doi:10.1016/j.xpro.2021.100820

Using EuGeneCiD and EuGeneCiM computational tools for synthetic biology

STAR Protoc. 2021 Sep 17;2(4):100820. doi: 10.1016/j.xpro.2021.100820. eCollection 2021 Dec 17.

Authors

Wheaton L Schroeder^{1

2}, Anna S Baber^{2

3}, Rajib Saha^{1

2}

Affiliations

¹ Department of Chemical and Biomolecular Engineering, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
² Center for Root and Rhizobiome Innovation, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
³ Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA.

Abstract

Synthetic biology often relies on the design of genetic circuits, utilizing "bioparts" (modular DNA pieces) to accomplish desired responses to external stimuli. While such designs are usually intuited, detailed here is a computational approach to synthetic biology design and modeling using optimization-based tools named Eukaryotic Genetic Circuit Design and Modeling. These allow for designing and subsequent screening of genetic circuits to increase the chances of in vivo success and contribute to the development of an application development pipeline. For complete details on the use and execution of this protocol, please refer to Schroeder, Baber, and Saha (2021).

Keywords: Biotechnology and bioengineering; Systems biology.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gene Regulatory Networks / genetics*
Humans
Models, Genetic*
Software*
Synthetic Biology / methods*